One Prompt Fits All: Universal Graph Adaptation for Pretrained Models
Abstract
Graph Prompt Learning (GPL) has emerged as a promising paradigm that bridges graph pretraining models and downstream scenarios, mitigating label dependency and the misalignment between upstream pretraining and downstream tasks. Although existing GPL studies explore various prompt strategies, their effectiveness and underlying principles remain unclear. We identify two critical limitations: (1) Lack of consensus on underlying mechanisms: Despite current GPLs have advanced the field, there is no consensus on how prompts interact with pretrained models, as different strategies intervene at varying spaces within the model, i.e., input-level, layer-wise, and representation-level prompts. (2) Limited scenario adaptability: Most methods fail to generalize across diverse downstream scenarios, especially under data distribution shifts (e.g., homophilic-to-heterophilic graphs). To address these issues, we theoretically analyze existing GPL approaches and reveal that representation-level prompts essentially function as fine-tuning a simple downstream classifier, proposing that graph prompt learning should focus on unleashing the capability of pretrained models, and the classifier should adapt to downstream scenarios. Based on our findings, we propose UniPrompt, a novel GPL method that adapts any pretrained models, unleashing the capability of pretrained models while preserving the input graph. Extensive experiments demonstrate that our method can effectively integrate with various pretrained models and achieve strong performance across in-domain and cross-domain scenarios.
Benchmark Results
Tested on 7 datasets 5 baseline values reported too low
Tables show presented results in global context (best 3 papers + GCN + MLP).
Classic
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GraphSAGE+CNA | 0.9418
±0.0033 | |
| 2 | GCN+CNA | 0.9366
±0.0048 | |
| 3 | TransformerConv | 0.9350
±0.0058 | |
| 21 | GCN | 0.9004 | |
| 724 | MLP | 0.7768 | |
| 884 | GPF | 0.5760
±0.1388 best reported | best at pub: GCoT: Chain-of-Thought Prompt Learning for Graphs (KDD 2025) Difference within reported uncertainty; not counted as underperformance. |
| 892 | GraphPrompt | 0.5425
±0.0938 best reported | best at pub: GCoT: Chain-of-Thought Prompt Learning for Graphs (KDD 2025) Difference within reported uncertainty; not counted as underperformance. |
| 898 | All-In-One | 0.5239
±0.1017 best reported | best at pub: ProG: A Graph Prompt Learning Benchmark (NeurIPS 2024) |
| 900 | Fine-tune | 0.5022
±0.0928 | This paper |
| 901 | Linear-probe | 0.5013
±0.1206 | This paper |
| 902 | UniPrompt | 0.4995
±0.1048 | This paper |
| 906 | EdgePrompt+ | 0.4532
±0.0903 | This paper |
| 909 | GPPT | 0.4315
±0.0944 best reported | best at pub: ProG: A Graph Prompt Learning Benchmark (NeurIPS 2024) Difference within reported uncertainty; not counted as underperformance. |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | CNA | 0.9575
±0.0058 | |
| 2 | IS-GIB | 0.9390
±0.0187 | |
| 3 | EERM | 0.9112
±0.0145 | |
| 44 | GCN | 0.8033
±0.0088 | |
| 350 | MLP | 0.7289
±0.0010 | |
| 603 | GPPT | 0.7031
±0.0039 best reported | |
| 866 | EdgePrompt+ | 0.4971
±0.0225 best reported | best today: MAGPrompt: Message-Adaptive Graph Prompt Tuning for Graph Neural Networks (2026) |
| 868 | UniPrompt | 0.4929
±0.1120 | This paper |
| 869 | GPF | 0.4489
±0.0661 | prev best: GCoT: Chain-of-Thought Prompt Learning for Graphs (KDD 2025) Improvement within reported uncertainty; not highlighted. |
| 870 | Linear-probe | 0.4808
±0.0696 | This paper |
| 871 | GraphPrompt | 0.4707
±0.0309 best reported | best at pub: GCoT: Chain-of-Thought Prompt Learning for Graphs (KDD 2025) best today: MAGPrompt: Message-Adaptive Graph Prompt Tuning for Graph Neural Networks (2026) Difference within reported uncertainty; not counted as underperformance. |
| 874 | Fine-tune | 0.4616
±0.0630 | This paper |
| 882 | All-In-One | 0.4436
±0.0252 best reported | best at pub: ProG: A Graph Prompt Learning Benchmark (NeurIPS 2024) best today: MAGPrompt: Message-Adaptive Graph Prompt Tuning for Graph Neural Networks (2026) |
Heterophilic Graphs
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | P^2GNN | 0.9672
±0.0147 | |
| 2 | DoG | 0.9660
±0.0210 | |
| 3 | GPF-plus | 0.9583
±0.0419 | |
| 34 | MLP | 0.9230
±0.0070 | |
| 53 | GraphSAGE | 0.9000
±0.0365 | |
| 100 | GPF | 0.8740
±0.0340 best reported | best at pub: ProG: A Graph Prompt Learning Benchmark (NeurIPS 2024) |
| 582 | UniPrompt | 0.4983
±0.1785 | This paper |
| 609 | Linear-probe | 0.3832
±0.1361 | This paper |
| 612 | Fine-tune | 0.3750
±0.1357 | This paper |
| 614 | GPPT | 0.3516
±0.1512 | This paper |
| 615 | EdgePrompt+ | 0.3502
±0.1661 | This paper |
| 617 | All-In-One | 0.3153
±0.1314 | prev best: Aligning the Spectrum: Hybrid Graph Pre-training and Prompt Tuning across Homophily and Heterophily (2025) Improvement within reported uncertainty; not highlighted. |
| 618 | GraphPrompt | 0.3019
±0.1363 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | P^2GNN | 0.9541
±0.0272 | |
| 2 | ACM-GCN | 0.9480
±0.0380 | |
| 3 | RF-GCN | 0.9429 | |
| 24 | MLP | 0.9136
±0.0070 | |
| 138 | SAGE | 0.8269 | |
| 459 | UniPrompt | 0.5280
±0.1108 | This paper |
| 560 | GPF | 0.3622
±0.0946 best reported | best today: Learning Graph Foundation Models on Riemannian Graph-of-Graphs (ICML 2026) Difference within reported uncertainty; not counted as underperformance. |
| 562 | Fine-tune | 0.3582
±0.1130 | This paper |
| 563 | GPPT | 0.2901
±0.0832 | |
| 564 | Linear-probe | 0.3492
±0.0974 | This paper |
| 567 | GraphPrompt | 0.3243
±0.1081 best reported | best today: Learning Graph Foundation Models on Riemannian Graph-of-Graphs (ICML 2026) Difference within reported uncertainty; not counted as underperformance. |
| 568 | EdgePrompt+ | 0.3213
±0.0742 | This paper |
| 573 | All-In-One | 0.2667
±0.1242 | prev best: Aligning the Spectrum: Hybrid Graph Pre-training and Prompt Tuning across Homophily and Heterophily (2025) Improvement within reported uncertainty; not highlighted. |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | DiGGR | 0.4535
±0.0353 | |
| 2 | TRIGON | 0.4402
±0.0028 | |
| 3 | DoG | 0.4320
±0.0120 | |
| 42 | MLP | 0.4026
±0.0108 | |
| 68 | GraphSAGE | 0.3899
±0.0085 | |
| 382 | GPF | 0.2870
±0.0335 best reported | best at pub: ProG: A Graph Prompt Learning Benchmark (NeurIPS 2024) |
| 419 | UniPrompt | 0.2623
±0.0446 | This paper |
| 440 | All-In-One | 0.2461
±0.0280 best reported | best at pub: ProG: A Graph Prompt Learning Benchmark (NeurIPS 2024) Difference within reported uncertainty; not counted as underperformance. |
| 462 | GPPT | 0.2258
±0.0197 best reported | best at pub: ProG: A Graph Prompt Learning Benchmark (NeurIPS 2024) Difference within reported uncertainty; not counted as underperformance. |
| 478 | Fine-tune | 0.2136
±0.0328 | This paper |
| 479 | EdgePrompt+ | 0.2136
±0.0276 | This paper |
| 480 | Linear-probe | 0.2133
±0.0262 | This paper |
| 488 | GraphPrompt | 0.1984
±0.0279 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | Hetero-S (GAT 8-layer) | 0.8693 | |
| 2 | Dir-GNN+CNA | 0.8586
±0.0180 | |
| 3 | GAT | 0.8560 | |
| 52 | GCN | 0.7033 | |
| 169 | MLP | 0.5429 | |
| 276 | GraphPrompt | 0.2828
±0.0438 | prev best: GCoT: Chain-of-Thought Prompt Learning for Graphs (KDD 2025) Improvement within reported uncertainty; not highlighted. |
| 280 | UniPrompt | 0.2667
±0.0251 | This paper |
| 281 | Fine-tune | 0.2622
±0.0273 | This paper |
| 282 | GPF | 0.2612
±0.0375 best reported | best at pub: GCoT: Chain-of-Thought Prompt Learning for Graphs (KDD 2025) Difference within reported uncertainty; not counted as underperformance. |
| 284 | GPPT | 0.2546
±0.0543 | This paper |
| 285 | Linear-probe | 0.2427
±0.0384 | This paper |
| 286 | EdgePrompt+ | 0.2379
±0.0331 | This paper |
| 288 | All-In-One | 0.2241
±0.0358 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | IBG-NN | 0.7763
±0.0179 | |
| 2 | Dir-GNN+CNA | 0.7747
±0.0128 | |
| 3 | DHGNN | 0.7684
±0.0161 | |
| 46 | GCN | 0.6067 | |
| 172 | MLP | 0.3930
±0.0079 | |
| 267 | UniPrompt | 0.2420
±0.0235 | This paper |
| 270 | GraphPrompt | 0.2285
±0.0328 | This paper |
| 272 | Linear-probe | 0.2282
±0.0410 | This paper |
| 275 | Fine-tune | 0.2227
±0.0410 | This paper |
| 277 | All-In-One | 0.2203
±0.0246 | This paper |
| 278 | EdgePrompt+ | 0.2199
±0.0250 | This paper |
| 279 | GPF | 0.2166
±0.0328 | This paper |
| 280 | GPPT | 0.2156
±0.0230 | This paper |
